Whole Genome Characterization of the Mechanisms of Daptomycin Resistance in Clinical and Laboratory Derived Isolates of <em>Staphylococcus aureus</em>

<div><h3>Background</h3><p>Daptomycin remains one of our last-line anti-staphylococcal agents. This study aims to characterize the genetic evolution to daptomycin resistance in <em>S. aureus</em>.</p> <h3>Methods</h3><p>Whole genome sequencing was performed on a unique collection of isogenic, clinical (21 strains) and laboratory (12 strains) derived strains that had been exposed to daptomycin and developed daptomycin-nonsusceptibility. Electron microscopy (EM) and lipid membrane studies were performed on selected isolates.</p> <h3>Results</h3><p>On average, six coding region mutations were observed across the genome in the clinical daptomycin exposed strains, whereas only two mutations on average were seen in the laboratory exposed pairs. All daptomycin-nonsusceptible strains had a mutation in a phospholipid biosynthesis gene. This included mutations in the previously described <em>mprF</em> gene, but also in other phospholipid biosynthesis genes, including cardiolipin synthase (<em>cls2</em>) and CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase (<em>pgsA</em>). EM and lipid membrane composition analyses on two clinical pairs showed that the daptomycin-nonsusceptible strains had a thicker cell wall and an increase in membrane lysyl-phosphatidylglycerol.</p> <h3>Conclusion</h3><p>Point mutations in genes coding for membrane phospholipids are associated with the development of reduced susceptibility to daptomycin in <em>S. aureus</em>. Mutations in <em>cls2</em> and <em>pgsA</em> appear to be new genetic mechanisms affecting daptomycin susceptibility in <em>S. aureus</em>.</p>